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- EMDB-13184: Subtomogram average of Axonemal Doublet Microtubule from Tetrahym... -

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Basic information

Entry
Database: EMDB / ID: EMD-13184
TitleSubtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila
Map dataSubtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila
Sample
  • Complex: Axonemal Doublet Microtubule from Tetrahymena thermophila
Biological speciesTetrahymena thermophila CU428 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 12.3 Å
AuthorsFernandez JJ / Li S
CitationJournal: J Struct Biol / Year: 2021
Title: TomoAlign: A novel approach to correcting sample motion and 3D CTF in CryoET.
Authors: Jose-Jesus Fernandez / Sam Li /
Abstract: TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) ...TomoAlign is a software package that integrates tools to mitigate two important resolution limiting factors in cryoET, namely the beam-induced sample motion and the contrast transfer function (CTF) of the microscope. The package is especially focused on cryoET of thick specimens where fiducial markers are required for accurate tilt-series alignment and sample motion estimation. TomoAlign models the beam-induced sample motion undergone during the tilt-series acquisition. The motion models are used to produce motion-corrected subtilt-series centered on the particles of interest. In addition, the defocus of each particle at each tilt image is determined and can be corrected, resulting in motion-corrected and CTF-corrected subtilt-series from which the subtomograms can be computed. Alternatively, the CTF information can be passed on so that CTF correction can be carried out entirely within external packages like Relion. TomoAlign serves as a versatile tool that can streamline the cryoET workflow from initial alignment of tilt-series to final subtomogram averaging during in situ structure determination.
History
DepositionJul 8, 2021-
Header (metadata) releaseSep 15, 2021-
Map releaseSep 15, 2021-
UpdateSep 15, 2021-
Current statusSep 15, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13184.png

Downloads & links

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Map

FileDownload / File: emd_13184.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of Axonemal Doublet Microtubule from Tetrahymena thermophila
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.3 Å/pix.
x 140 pix.
= 742. Å		5.3 Å/pix.
x 140 pix.
= 742. Å		5.3 Å/pix.
x 140 pix.
= 742. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.2943295 - 0.6126081
Average (Standard dev.)0.007897773 (±0.06800612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 742.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.35.35.3
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z742.000742.000742.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.2940.6130.008

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Supplemental data

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Sample components

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Entire : Axonemal Doublet Microtubule from Tetrahymena thermophila

EntireName: Axonemal Doublet Microtubule from Tetrahymena thermophila
Components
  • Complex: Axonemal Doublet Microtubule from Tetrahymena thermophila

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Supramolecule #1: Axonemal Doublet Microtubule from Tetrahymena thermophila

SupramoleculeName: Axonemal Doublet Microtubule from Tetrahymena thermophila
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila CU428 (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 9540
ExtractionNumber tomograms: 24 / Number images used: 9540
Final angle assignmentType: OTHER

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